1
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Tranter D, Paatero AO, Kawaguchi S, Kazemi S, Serrill JD, Kellosalo J, Vogel WK, Richter U, Mattos DR, Wan X, Thornburg CC, Oishi S, McPhail KL, Ishmael JE, Paavilainen VO. Coibamide A Targets Sec61 to Prevent Biogenesis of Secretory and Membrane Proteins. ACS Chem Biol 2020; 15:2125-2136. [PMID: 32608972 PMCID: PMC7497630 DOI: 10.1021/acschembio.0c00325] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 07/01/2020] [Indexed: 01/19/2023]
Abstract
Coibamide A (CbA) is a marine natural product with potent antiproliferative activity against human cancer cells and a unique selectivity profile. Despite promising antitumor activity, the mechanism of cytotoxicity and specific cellular target of CbA remain unknown. Here, we develop an optimized synthetic CbA photoaffinity probe (photo-CbA) and use it to demonstrate that CbA directly targets the Sec61α subunit of the Sec61 protein translocon. CbA binding to Sec61 results in broad substrate-nonselective inhibition of ER protein import and potent cytotoxicity against specific cancer cell lines. CbA targets a lumenal cavity of Sec61 that is partially shared with known Sec61 inhibitors, yet profiling against resistance conferring Sec61α mutations identified from human HCT116 cells suggests a distinct binding mode for CbA. Specifically, despite conferring strong resistance to all previously known Sec61 inhibitors, the Sec61α mutant R66I remains sensitive to CbA. A further unbiased screen for Sec61α resistance mutations identified the CbA-resistant mutation S71P, which confirms nonidentical binding sites for CbA and apratoxin A and supports the susceptibility of the Sec61 plug region for channel inhibition. Remarkably, CbA, apratoxin A, and ipomoeassin F do not display comparable patterns of potency and selectivity in the NCI60 panel of human cancer cell lines. Our work connecting CbA activity with selective prevention of secretory and membrane protein biogenesis by inhibition of Sec61 opens up possibilities for developing new Sec61 inhibitors with improved drug-like properties that are based on the coibamide pharmacophore.
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Affiliation(s)
- Dale Tranter
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland
| | - Anja O. Paatero
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland
| | - Shinsaku Kawaguchi
- Graduate
School of Pharmaceutical Sciences, Kyoto
University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Soheila Kazemi
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Jeffrey D. Serrill
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Juho Kellosalo
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland
| | - Walter K. Vogel
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Uwe Richter
- Molecular
and Integrative Biosciences Research Programme, Faculty of Biological
and Environmental Sciences, University of
Helsinki, Helsinki, 00014, Finland
| | - Daphne R. Mattos
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Xuemei Wan
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Christopher C. Thornburg
- Frederick
National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 21702, United States
| | - Shinya Oishi
- Graduate
School of Pharmaceutical Sciences, Kyoto
University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kerry L. McPhail
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Jane E. Ishmael
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
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2
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Zong G, Hu Z, O’Keefe S, Tranter D, Iannotti MJ, Baron L, Hall B, Corfield K, Paatero AO, Henderson MJ, Roboti P, Zhou J, Sun X, Govindarajan M, Rohde JM, Blanchard N, Simmonds R, Inglese J, Du Y, Demangel C, High S, Paavilainen VO, Shi WQ. Ipomoeassin F Binds Sec61α to Inhibit Protein Translocation. J Am Chem Soc 2019; 141:8450-8461. [PMID: 31059257 PMCID: PMC6627486 DOI: 10.1021/jacs.8b13506] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Ipomoeassin F is a potent natural cytotoxin that inhibits growth of many tumor cell lines with single-digit nanomolar potency. However, its biological and pharmacological properties have remained largely unexplored. Building upon our earlier achievements in total synthesis and medicinal chemistry, we used chemical proteomics to identify Sec61α (protein transport protein Sec61 subunit alpha isoform 1), the pore-forming subunit of the Sec61 protein translocon, as a direct binding partner of ipomoeassin F in living cells. The interaction is specific and strong enough to survive lysis conditions, enabling a biotin analogue of ipomoeassin F to pull down Sec61α from live cells, yet it is also reversible, as judged by several experiments including fluorescent streptavidin staining, delayed competition in affinity pulldown, and inhibition of TNF biogenesis after washout. Sec61α forms the central subunit of the ER protein translocation complex, and the binding of ipomoeassin F results in a substantial, yet selective, inhibition of protein translocation in vitro and a broad ranging inhibition of protein secretion in live cells. Lastly, the unique resistance profile demonstrated by specific amino acid single-point mutations in Sec61α provides compelling evidence that Sec61α is the primary molecular target of ipomoeassin F and strongly suggests that the binding of this natural product to Sec61α is distinctive. Therefore, ipomoeassin F represents the first plant-derived, carbohydrate-based member of a novel structural class that offers new opportunities to explore Sec61α function and to further investigate its potential as a therapeutic target for drug discovery.
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Affiliation(s)
- Guanghui Zong
- †Department
of Chemistry and Biochemistry and ⬡Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States,Department
of Chemistry and Biochemistry, University
of Maryland, College Park, Maryland 20742, United States
| | - Zhijian Hu
- †Department
of Chemistry and Biochemistry and ⬡Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Sarah O’Keefe
- School
of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, United Kingdom
| | - Dale Tranter
- University
of Helsinki, HiLIFE, Helsinki, Finland,Institute
of Biotechnology, Helsinki, Finland
| | - Michael J. Iannotti
- National
Center for Advancing Translational Sciences, National
Institutes of Health, Rockville, Maryland 20850, United States
| | - Ludivine Baron
- Immunobiology
of Infection Unit, Institut Pasteur, 75015 Paris, France,INSERM, U1221, 75005 Paris, France
| | - Belinda Hall
- Department
of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, Surrey GU2 7XH, United Kingdom
| | - Katherine Corfield
- Department
of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, Surrey GU2 7XH, United Kingdom
| | - Anja O. Paatero
- University
of Helsinki, HiLIFE, Helsinki, Finland,Institute
of Biotechnology, Helsinki, Finland
| | - Mark J. Henderson
- National
Center for Advancing Translational Sciences, National
Institutes of Health, Rockville, Maryland 20850, United States
| | - Peristera Roboti
- School
of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, United Kingdom
| | - Jianhong Zhou
- †Department
of Chemistry and Biochemistry and ⬡Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Xianwei Sun
- †Department
of Chemistry and Biochemistry and ⬡Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States,Department
of Radiology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Mugunthan Govindarajan
- †Department
of Chemistry and Biochemistry and ⬡Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States,Emory
Institute for Drug Development, Emory University, 954 Gatewood Road, Atlanta, Georgia 30329, United States
| | - Jason M. Rohde
- National
Center for Advancing Translational Sciences, National
Institutes of Health, Rockville, Maryland 20850, United States
| | - Nicolas Blanchard
- Université
de Haute-Alsace, Université de Strasbourg, CNRS, LIMA, UMR 7042, 68000 Mulhouse, France
| | - Rachel Simmonds
- Department
of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, Surrey GU2 7XH, United Kingdom,
| | - James Inglese
- National
Center for Advancing Translational Sciences, National
Institutes of Health, Rockville, Maryland 20850, United States,
| | - Yuchun Du
- †Department
of Chemistry and Biochemistry and ⬡Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States,
| | - Caroline Demangel
- Immunobiology
of Infection Unit, Institut Pasteur, 75015 Paris, France,INSERM, U1221, 75005 Paris, France,
| | - Stephen High
- School
of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, United Kingdom,
| | - Ville O. Paavilainen
- University
of Helsinki, HiLIFE, Helsinki, Finland,Institute
of Biotechnology, Helsinki, Finland,
| | - Wei Q. Shi
- †Department
of Chemistry and Biochemistry and ⬡Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States,Department
of Chemistry, Ball State University, Muncie, Indiana 47306, United States,;
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3
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Morel JD, Paatero AO, Wei J, Yewdell JW, Guenin-Macé L, Van Haver D, Impens F, Pietrosemoli N, Paavilainen VO, Demangel C. Proteomics Reveals Scope of Mycolactone-mediated Sec61 Blockade and Distinctive Stress Signature. Mol Cell Proteomics 2018; 17:1750-1765. [PMID: 29915147 DOI: 10.1074/mcp.ra118.000824] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 06/17/2018] [Indexed: 11/06/2022] Open
Abstract
Mycolactone is a bacteria-derived macrolide that blocks the biogenesis of a large array of secretory and integral transmembrane proteins (TMP) through potent inhibition of the Sec61 translocon. Here, we used quantitative proteomics to delineate the direct and indirect effects of mycolactone-mediated Sec61 blockade in living cells. In T lymphocytes, dendritic cells and sensory neurons, Sec61 substrates downregulated by mycolactone were in order of incidence: secretory proteins (with a signal peptide but no transmembrane domain), TMPs with a signal peptide (Type I) and TMPs without signal peptide and a cytosolic N terminus (Type II). TMPs without a signal peptide and the opposite N terminus topology (Type III) were refractory to mycolactone inhibition. This rule applied comparably to single- and multi-pass TMPs, and extended to exogenous viral proteins. Parallel to its broad-spectrum inhibition of Sec61-mediated protein translocation, mycolactone rapidly induced cytosolic chaperones Hsp70/Hsp90. Moreover, it activated an atypical endoplasmic reticulum stress response, differing from conventional unfolded protein response by the down-regulation of Bip. In addition to refining our mechanistic understanding of Sec61 inhibition by mycolactone, our findings thus reveal that Sec61 blockade induces proteostatic stress in the cytosol and the endoplasmic reticulum.
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Affiliation(s)
- Jean-David Morel
- From the ‡Immunobiology of Infection Unit, Institut Pasteur, 75015 Paris, France.,§INSERM, U1221, 75005 Paris, France
| | - Anja O Paatero
- ¶Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Jiajie Wei
- ‖Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Jonathan W Yewdell
- ‖Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Laure Guenin-Macé
- From the ‡Immunobiology of Infection Unit, Institut Pasteur, 75015 Paris, France.,§INSERM, U1221, 75005 Paris, France
| | - Delphi Van Haver
- **VIB-UGent Center for Medical Biotechnology, 9000 Ghent, Belgium.,‡‡VIB Proteomics Core, 9000 Ghent, Belgium.,§§Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Francis Impens
- **VIB-UGent Center for Medical Biotechnology, 9000 Ghent, Belgium.,‡‡VIB Proteomics Core, 9000 Ghent, Belgium.,§§Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Natalia Pietrosemoli
- ¶¶Bioinformatics and Biostatistics Hub, Center of Bioinformatics, Biostatistics, and Integrative Biology, Institut Pasteur, Unité de Service et de Recherche 3756 Institut Pasteur CNRS, 75015 Paris, France
| | - Ville O Paavilainen
- ¶Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Caroline Demangel
- From the ‡Immunobiology of Infection Unit, Institut Pasteur, 75015 Paris, France; .,§INSERM, U1221, 75005 Paris, France
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4
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Paatero AO, Kellosalo J, Dunyak BM, Almaliti J, Gestwicki JE, Gerwick WH, Taunton J, Paavilainen VO. Apratoxin Kills Cells by Direct Blockade of the Sec61 Protein Translocation Channel. Cell Chem Biol 2017; 23:561-566. [PMID: 27203376 DOI: 10.1016/j.chembiol.2016.04.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 04/04/2016] [Accepted: 04/07/2016] [Indexed: 12/17/2022]
Abstract
Apratoxin A is a cytotoxic natural product that prevents the biogenesis of secretory and membrane proteins. Biochemically, apratoxin A inhibits cotranslational translocation into the ER, but its cellular target and mechanism of action have remained controversial. Here, we demonstrate that apratoxin A prevents protein translocation by directly targeting Sec61α, the central subunit of the protein translocation channel. Mutagenesis and competitive photo-crosslinking studies indicate that apratoxin A binds to the Sec61 lateral gate in a manner that differs from cotransin, a substrate-selective Sec61 inhibitor. In contrast to cotransin, apratoxin A does not exhibit a substrate-selective inhibitory mechanism, but blocks ER translocation of all tested Sec61 clients with similar potency. Our results suggest that multiple structurally unrelated natural products have evolved to target overlapping but non-identical binding sites on Sec61, thereby producing distinct biological outcomes.
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Affiliation(s)
- Anja O Paatero
- Institute of Biotechnology, University of Helsinki, Viikinkaari 1, Biocenter 3, Helsinki 00014, Finland
| | - Juho Kellosalo
- Institute of Biotechnology, University of Helsinki, Viikinkaari 1, Biocenter 3, Helsinki 00014, Finland
| | - Bryan M Dunyak
- Department of Pharmaceutical Chemistry, Institute for Neurodegenerative Disease, University of California at San Francisco, San Francisco, CA 94038, USA
| | - Jehad Almaliti
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry, Institute for Neurodegenerative Disease, University of California at San Francisco, San Francisco, CA 94038, USA
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA 94158, USA
| | - Ville O Paavilainen
- Institute of Biotechnology, University of Helsinki, Viikinkaari 1, Biocenter 3, Helsinki 00014, Finland.
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5
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Paatero AO, Turakainen H, Happonen LJ, Olsson C, Palomäki T, Pajunen MI, Meng X, Otonkoski T, Tuuri T, Berry C, Malani N, Frilander MJ, Bushman FD, Savilahti H. Bacteriophage Mu integration in yeast and mammalian genomes. Nucleic Acids Res 2008; 36:e148. [PMID: 18953026 PMCID: PMC2602771 DOI: 10.1093/nar/gkn801] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Revised: 10/09/2008] [Accepted: 10/10/2008] [Indexed: 11/14/2022] Open
Abstract
Genomic parasites have evolved distinctive lifestyles to optimize replication in the context of the genomes they inhabit. Here, we introduced new DNA into eukaryotic cells using bacteriophage Mu DNA transposition complexes, termed 'transpososomes'. Following electroporation of transpososomes and selection for marker gene expression, efficient integration was verified in yeast, mouse and human genomes. Although Mu has evolved in prokaryotes, strong biases were seen in the target site distributions in eukaryotic genomes, and these biases differed between yeast and mammals. In Saccharomyces cerevisiae transposons accumulated outside of genes, consistent with selection against gene disruption. In mouse and human cells, transposons accumulated within genes, which previous work suggests is a favorable location for efficient expression of selectable markers. Naturally occurring transposons and viruses in yeast and mammals show related, but more extreme, targeting biases, suggesting that they are responding to the same pressures. These data help clarify the constraints exerted by genome structure on genomic parasites, and illustrate the wide utility of the Mu transpososome technology for gene transfer in eukaryotic cells.
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Affiliation(s)
- Anja O. Paatero
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Hilkka Turakainen
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Lotta J. Happonen
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Cia Olsson
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Tiina Palomäki
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Maria I. Pajunen
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Xiaojuan Meng
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Timo Otonkoski
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Timo Tuuri
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Charles Berry
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Nirav Malani
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Mikko J. Frilander
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Frederic D. Bushman
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Harri Savilahti
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
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6
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Pirttimaa MJ, Paatero AO, Frilander MJ, Bamford DH. Nonspecific nucleoside triphosphatase P4 of double-stranded RNA bacteriophage phi6 is required for single-stranded RNA packaging and transcription. J Virol 2002; 76:10122-7. [PMID: 12239286 PMCID: PMC136547 DOI: 10.1128/jvi.76.20.10122-10127.2002] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteriophage phi6 has a segmented double-stranded RNA genome. The genomic single-stranded RNA (ssRNA) precursors are packaged into a preformed protein capsid, the polymerase complex, composed of viral proteins P1, P2, P4, and P7. Packaging of the genomic precursors is an energy-dependent process requiring nucleoside triphosphates. Protein P4, a nonspecific nucleoside triphosphatase, has previously been suggested to be the prime candidate for the viral packaging engine, based on its location at the vertices of the viral capsid and its biochemical characteristics. In this study we were able to obtain stable polymerase complex particles that are completely devoid of P4. Such particles were not able to package ssRNA segments and did not display RNA polymerase (either minus- or plus-strand synthesis) activity. Surprisingly, a mutation in P4, S250Q, which reduced the level of P4 in the particles to about 10% of the wild-type level, did not affect RNA packaging activity or change the kinetics of packaging. Moreover, such particles displayed minus-strand synthesis activity. However, no plus-strand synthesis was observed, suggesting that P4 has a role in the plus-strand synthesis reaction also.
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Affiliation(s)
- Markus J Pirttimaa
- Department of Biosciences. Institute of Biotechnology, Viikki Biocenter, FIN-00014 University of Helsinki, Finland
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7
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Abstract
We present the assembly of the polymerase complex (procapsid) of a dsRNA virus from purified recombinant proteins. This molecular machine packages and replicates viral ssRNA genomic precursors in vitro. After addition of an external protein shell, these in vitro self-assembled viral core particles can penetrate the host plasma membrane and initiate a productive infection. Thus, a viral procapsid has been assembled and rendered infectious using purified components. Using this system, we have studied the mechanism of assembly of the common dsRNA virus shell and the incorporation of a symmetry mismatch within an icosahedral capsid. Our work demonstrates that this molecular machine, self-assembled under defined conditions in vitro, can function in its natural environment, the cell cytoplasm.
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Affiliation(s)
- M M Poranen
- Department of Biosciences, University of Helsinki, 00014 Helsinki, Finland
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8
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de Haas F, Paatero AO, Mindich L, Bamford DH, Fuller SD. A symmetry mismatch at the site of RNA packaging in the polymerase complex of dsRNA bacteriophage phi6. J Mol Biol 1999; 294:357-72. [PMID: 10610764 DOI: 10.1006/jmbi.1999.3260] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The polymerase complex of the enveloped double-stranded RNA (dsRNA) bacteriophage phi6 fulfils a similar function to those of other dsRNA viruses such as Reoviridae. The phi6 complex comprises protein P1, which forms the shell, and proteins P2, P4 and P7, which are involved in RNA synthesis and packaging. Icosahedral reconstructions from cryo-electron micrographs of recombinant polymerase particles revealed a clear dodecahedral shell and weaker satellites. Difference imaging demonstrated that these weak satellites were the sites of P4 and P2 within the complex. The structure determined by icosahedral reconstruction was used as an initial model in an iterative reconstruction technique to examine the departures from icosahedral symmetry. This approach showed that P4 and P2 contribute to structures at the 5-fold positions of the icosahedral P1 shell which lack 5-fold symmetry and appear in variable orientations. Reconstruction of isolated recombinant P4 showed that it was a hexamer with a size and shape matching the satellite. Symmetry mismatch between the satellites and the shell could play a role in RNA packaging akin to that of the portal vertex of dsDNA phages in DNA packaging. This is the first example of dsRNA virus in which the structure of the polymerase complex has been determined without the assumption of icosahedral symmetry. Our result with phi6 illustrates the symmetry mismatch which may occur at the sites of RNA packaging in other dsRNA viruses such as members of the Reoviridae.
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Affiliation(s)
- F de Haas
- The Structural Biology Programme, European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, 69117, Germany
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Paatero AO, Mindich L, Bamford DH. Mutational analysis of the role of nucleoside triphosphatase P4 in the assembly of the RNA polymerase complex of bacteriophage phi6. J Virol 1998; 72:10058-65. [PMID: 9811745 PMCID: PMC110533 DOI: 10.1128/jvi.72.12.10058-10065.1998] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/1998] [Accepted: 08/25/1998] [Indexed: 11/20/2022] Open
Abstract
Bacteriophage phi6 is a complex enveloped double-stranded RNA virus with a segmented genome and replication strategy quite similar to that of the Reoviridae. An in vitro packaging and replication system using purified components is available. The positive-polarity genomic segments are translocated into a preformed polymerase complex (procapsid) particle. This particle is composed of four proteins: the shell-forming protein P1, the RNA polymerase P2, and two proteins active in packaging. Protein P7 is involved in stable packaging, and protein P4 is a homomultimeric potent nucleoside triphosphatase that provides the energy for the RNA translocation event. In this investigation, we used mutational analysis to study P4 multimerization and assembly. P4 is assembled onto a preformed particle containing proteins P2 and P7 in addition to P1. Only simultaneous production of P1 and P4 in the same cell leads to P4 assembly on P1 alone, whereas the P1 shell is incompetent for accepting P4 if produced separately. The C-terminal part of P4 is essential for particle assembly but not for multimerization or enzymatic activity. Altering the P4 nucleoside triphosphate binding site destroys the ability to form multimers.
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Affiliation(s)
- A O Paatero
- Department of Biosciences, Biocenter, FIN-00014, University of Helsinki, Finland
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Paatero AO, Syväoja JE, Bamford DH. Double-stranded RNA bacteriophage phi 6 protein P4 is an unspecific nucleoside triphosphatase activated by calcium ions. J Virol 1995; 69:6729-34. [PMID: 7474083 PMCID: PMC189583 DOI: 10.1128/jvi.69.11.6729-6734.1995] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Double-stranded RNA bacteriophage phi 6 has an envelope surrounding the nucleocapsid (NC). The NC is composed of a surface protein, P8, and proteins P1, P2, P4, and P7, which form a dodecahedral polymerase complex enclosing the segmented viral genome. Empty polymerase complex particles (procapsids) package positive-sense viral single-stranded RNAs provided that energy is available in the form of nucleoside triphosphates (NTPs). Photoaffinity labelling of both the NC and the procapsid has earlier been used to show that ATP binds to protein P4 and that the NC hydrolyzes NTPs. Using the NC and the NC core particles (NCs lacking surface protein P8) and purified protein P4, we demonstrate here that multimeric P4 is the active NTPase. Isolation of multimeric P4 is successful only in the presence of NTPs. The activity of P4 is the same in association with the viral particles as it is in pure form. P4 is an unspecific NTPase hydrolyzing ribo-NTPs, deoxy NTPs, and dideoxy NTPs to the corresponding nucleoside diphosphates. The Km of the reaction for ATP, GTP, and UTP is around 0.2 to 0.3 mM. The NTP hydrolysis by P4 absolutely requires residual amounts of Mg2+ ions and is greatly activated when the Ca2+ concentration reaches 0.5 mM. Competition experiments indicate that Mg2+ and Ca2+ ions have approximately equal binding affinities for P4. They might compete for a common binding site. The nucleotide specificity and enzymatic properties of the P4 NTPase are similar to the NTP hydrolysis reaction conditions needed to translocate and condense the viral positive-sense RNAs to the procapsid particle.
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Affiliation(s)
- A O Paatero
- Department of Biosciences, University of Helsinki, Finland
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Abstract
Bacteriophage ø6 is a double-stranded RNA virus consisting of a nucleocapsid (NC) surrounded by a membrane. Beneath the NC major coat protein, P8, resides the ø6 RNA polymerase complex which is composed of four early proteins P1, P2, P4, and P7. Protein P1 forms the dodecahedral framework with which the other three proteins are associated. We have developed a new method for the isolation of stable polymerase complex particles which retain their structural integrity and polymerase activity for several days. Purine nucleotides, especially GTP, dGTP, ddGTP, and GDP, stabilized the particle efficiently. Furthermore, binding of any NTP was shown to induce conformational changes in the NC structure, as detected by alterations in the binding properties of NC-specific monoclonal antibodies. In the presence of NTPs, most of the epitopes in protein P4 become more exposed than without NTPs, while the epitopes in protein P8 were either masked or unmasked due to NTP binding. Based on the accessibility of the epitopes of protein P1 on the NC, we postulate that at least part of this protein is also accessible on the NC surface.
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Affiliation(s)
- P M Ojala
- Department of Genetics, University of Helsinki, Finland
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